102 results on '"PHAGE DISPLAY"'
Search Results
2. The type IV secretion system core component VirB8 interacts via the β1-strand with VirB10.
- Author
-
Sharifahmadian, Mahzad, Nlend, Ingrid U., Lecoq, Lauriane, Omichinski, James G., and Baron, Christian
- Subjects
- *
REGULATION of secretion , *SECRETION , *BIOLOGICAL transport , *NUCLEAR magnetic resonance , *EXCRETION , *PHYSIOLOGY - Abstract
In this work, we provide evidence for the interactions between VirB8 and VirB10, two core components of the type IV secretion system (T4SS). Using nuclear magnetic resonance experiments, we identified residues on the β1-strand of Brucella VirB8 that undergo chemical shift changes in the presence of VirB10. Bacterial two-hybrid experiments confirm the importance of the β1-strand, whereas phage display experiments suggest that the α2-helix of VirB8 may also contribute to the interaction with VirB10. Conjugation assays using the VirB8 homolog TraE as a model show that several residues on the β1-strand of TraE are important for T4SS function. Together, our results suggest that the β1-strand of VirB8-like proteins is essential for their interaction with VirB10 in the T4SS complex. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
3. Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin.
- Author
-
Garrido-Urbani, Sarah, Garg, Pankaj, Ghossoub, Rania, Arnold, Roland, Lembo, Frédérique, Sundell, Gustav N., Kim, Philip M., Lopez, Marc, Zimmermann, Pascale, Sidhu, Sachdev S., and Ivarsson, Ylva
- Subjects
- *
PROTEOMICS , *PEPTIDES , *CELL adhesion , *CELL migration , *PROTEIN-protein interactions - Abstract
Syntenin has crucial roles in cell adhesion, cell migration and synaptic transmission. Its closely linked postsynaptic density-95, discs large 1, zonula occludens-1 (PDZ) domains typically interact with C-terminal ligands. We profile syntenin PDZ1-2 through proteomic peptide phage display (ProP-PD) using a library that displays C-terminal regions of the human proteome. The protein recognizes a broad range of peptides, with a preference for hydrophobic motifs and has a tendency to recognize cryptic internal ligands. We validate the interaction with nectin-1 through orthogonal assays. The study demonstrates the power of ProP-PD as a complementary approach to uncover interactions of potential biological relevance. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
4. Phage protein-targeted cancer nanomedicines.
- Author
-
Petrenko, V.A. and Jayanna, P.K.
- Subjects
- *
NANOMEDICINE , *ANTINEOPLASTIC agents , *MICROENCAPSULATION , *IMMUNOGLOBULINS , *PEPTIDES , *FLUORESCENCE resonance energy transfer - Abstract
Abstract: Nanoencapsulation of anticancer drugs improves their therapeutic indices by virtue of the enhanced permeation and retention effect which achieves passive targeting of nanoparticles in tumors. This effect can be significantly enhanced by active targeting of nanovehicles to tumors. Numerous ligands have been proposed and used in various studies with peptides being considered attractive alternatives to antibodies. This is further reinforced by the availability of peptide phage display libraries which offer an unlimited reservoir of target-specific probes. In particular landscape phages with multivalent display of target-specific peptides which enable the phage particle itself to become a nanoplatform creates a paradigm for high throughput selection of nanoprobes setting the stage for personalized cancer management. Despite its promise, this conjugate of combinatorial chemistry and nanotechnology has not made a significant clinical impact in cancer management due to a lack of using robust processes that facilitate scale-up and manufacturing. To this end we proposed the use of phage fusion protein as the navigating modules of novel targeted nanomedicine platforms which are described in this review. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
5. Development of inhibitors in the ubiquitination cascade.
- Author
-
Zhang, Wei and Sidhu, Sachdev S.
- Subjects
- *
UBIQUITINATION , *UBIQUITIN , *NEURODEGENERATION , *PROTEASOME inhibitors , *CANCER treatment , *PROTEIN engineering , *DRUG development - Abstract
Abstract: The ubiquitin proteasome system (UPS) is essential in regulating myriad aspects of protein functions. It is therefore a fundamentally important regulatory mechanism that impacts most if not all aspects of cellular processes. Indeed, malfunction of UPS components is implicated in human diseases such as neurodegenerative and immunological disorders and many cancers. The success of proteasome inhibitors in cancer therapy suggests that modulating enzymes in the ubiquitination cascade would be clinically important for therapeutic benefits. In this review, we summarize advances in developing inhibitors of a variety of UPS components. In particular, we highlight recent work done on the protein engineering of ubiquitin as modulators of the UPS, a novel approach that may shed light on innovative drug discovery in the future. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
6. Profiling the IgOme: Meeting the challenge.
- Author
-
Weiss-Ottolenghi, Yael and Gershoni, Jonathan M.
- Subjects
- *
IMMUNOGLOBULINS , *BLOOD proteins , *IMMUNE system , *HOMEOSTASIS , *VACCINES , *DRUG development - Abstract
Abstract: The entire repertoire of antibodies in our serum, the IgOme, is a historical record of our past experiences and a reflection of our immune status at any given moment. Understanding the dynamics of the IgOme and how the diversity and specificities of serum antibodies change in response to disease and maintenance of homeostasis can directly impact the ability to design and develop novel vaccines, diagnostics and therapeutics. Here we review both direct and indirect methodologies that are being developed to map the complexity and specificities of the antibodies in polyclonal serum – the IgOme. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
7. NELL-1 binds to APR3 affecting human osteoblast proliferation and differentiation
- Author
-
Zou, Xuan, Shen, Jia, Chen, Feng, Ting, Kang, Zheng, Zhong, Pang, Shen, Zara, Janette N., Adams, John S., Soo, Chia, and Zhang, Xinli
- Subjects
- *
MEMBRANE proteins , *TRETINOIN , *APOPTOSIS , *ALKALINE phosphatase , *TRANSCRIPTION factors , *GENE expression , *CELL proliferation , *BONE cells , *CARRIER proteins - Abstract
Abstract: Nel-like protein 1 (NELL-1) is an osteoinductive molecule associated with premature calvarial suture closure. Here we identified apoptosis related protein 3 (APR3), a membrane protein known as a proliferation suppressor, as a binding protein of NELL-1 by biopanning. NELL-1 and APR3 colocalized on the nuclear envelope of human osteoblasts. NELL-1 significantly inhibited proliferation of osteoblasts co-transfected with APR3 through further down-regulation of Cyclin D1. The co-expression of NELL-1 and APR3 enhanced Ocn and Bsp expression and mineralization. RNAi of APR3 significantly reduced the differentiation effect of NELL-1. These findings suggest that the effects of NELL-1 on osteoblastic differentiation and proliferation are partly through binding to APR3. Structured summary of protein interactions: APR3 physically interacts with NELL1 by pull down (View interaction) APR3 and NELL1 colocalize by fluorescence microscopy (View interaction) NELL1 physically interacts with SMEK1 by phage display (View interaction) NELL1 physically interacts with EIF4B by phage display (View interaction) NELL1 physically interacts with APR3 by anti bait coimmunoprecipitation (View interaction) NELL1 physically interacts with EIF5B by phage display (View interaction) NELL1 physically interacts with DNTTIP2 by phage display (View interaction) NELL1 physically interacts with EEF1A1 by phage display (View interaction) NELL1 physically interacts with Nexilin by phage display (View interaction) NELL1 physically interacts with PLCG1 by phage display (View interaction) NELL1 physically interacts with APR3 by phage display (View interaction) NELL1 physically interacts with SLTM by phage display (View interaction) NELL1 physically interacts with SSRP1 by phage display (View interaction) NELL1 physically interacts with NOL10 by phage display (View interaction) [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
8. Affibody molecules: Engineered proteins for therapeutic, diagnostic and biotechnological applications
- Author
-
Löfblom, J., Feldwisch, J., Tolmachev, V., Carlsson, J., Ståhl, S., and Frejd, F.Y.
- Subjects
- *
MOLECULAR biology , *PROTEIN engineering , *GENE targeting , *SCAFFOLD proteins , *BIOTHERAPY , *BIOTECHNOLOGY - Abstract
Abstract: Affibody molecules are a class of engineered affinity proteins with proven potential for therapeutic, diagnostic and biotechnological applications. Affibody molecules are small (6.5kDa) single domain proteins that can be isolated for high affinity and specificity to any given protein target. Fifteen years after its discovery, the Affibody technology is gaining use in many groups as a tool for creating molecular specificity wherever a small, engineering compatible tool is warranted. Here we summarize recent results using this technology, propose an Affibody nomenclature and give an overview of different HER2-specific Affibody molecules. Cumulative evidence suggests that the three helical scaffold domain used as basis for these molecules is highly suited to create a molecular affinity handle for vastly different applications. [Copyright &y& Elsevier]
- Published
- 2010
- Full Text
- View/download PDF
9. Use of in vivo phage display to engineer novel adenoviruses for targeted delivery to the cardiac vasculature
- Author
-
Nicol, Campbell G., Denby, Laura, Lopez-Franco, Oscar, Masson, Rachel, Halliday, Crawford A., Nicklin, Stuart A., Kritz, Angelika, Work, Lorraine M., and Baker, Andrew H.
- Subjects
- *
CARDIOVASCULAR diseases , *BLOOD vessels , *ADENOVIRUSES , *ANIMAL models in research , *GENE targeting , *DRUG delivery systems , *VIRAL genetics - Abstract
Abstract: We performed in vivo phage display in the stroke prone spontaneously hypertensive rat, a cardiovascular disease model, and the normotensive Wistar Kyoto rat to identify cardiac targeting peptides, and then assessed each in the context of viral gene delivery. We identified both common and strain-selective peptides, potentially indicating ubiquitous markers and those found selectively in dysfunctional microvasculature of the heart. We show the utility of the peptide, DDTRHWG, for targeted gene delivery in human cells and rats in vivo when cloned into the fiber protein of subgroup D adenovirus 19p. This study therefore identifies cardiac targeting peptides by in vivo phage display and the potential of a candidate peptide for vector targeting strategies. [Copyright &y& Elsevier]
- Published
- 2009
- Full Text
- View/download PDF
10. Versatile retargeting of SH3 domain binding by modification of non-conserved loop residues
- Author
-
Hiipakka, Marita and Saksela, Kalle
- Subjects
- *
HOMOLOGY (Biology) , *IMMUNODEFICIENCY , *GENETIC engineering , *MICROBIAL genetics - Abstract
Abstract: Src-homology (SH3) domain belongs to a class of ubiquitous modular protein domains found in nature. SH3 domains have a conserved surface that recognises proline-rich peptides in ligand proteins, but additional contacts also contribute to binding. Using the SH3 domain of hematopoietic cell kinase as a test case, we show that SH3 binding properties can be profoundly altered by modifications within a hexapeptide sequence in the RT-loop region that is not involved in recognition of currently known consensus SH3 target peptides. These results highlight the role of non-conserved regions in SH3 target selection, and introduce a strategy that may be generally feasible for generating artificial SH3 domains with desired ligand binding properties. [Copyright &y& Elsevier]
- Published
- 2007
- Full Text
- View/download PDF
11. Identification of the HIV-1 gp41 core-binding motif – HXXNPF
- Author
-
Huang, Jing-He, Liu, Zu-Qiang, Liu, Shuwen, Jiang, Shibo, and Chen, Ying-Hua
- Subjects
- *
BIOLOGICAL membranes , *CELL membranes , *MOLECULAR cloning , *MONOCLONAL antibodies - Abstract
Abstract: The HIV-1 gp41 core, a six-helix bundle formed between the N- and C-terminal heptad repeats, plays a critical role in fusion between the viral and target cell membranes. Using N36(L8)C34 as a model of the gp41 core to screen phage display peptide libraries, we identified a common motif, HXXNPF (X is any of the 20 natural amino acid residues). A selected positive phage clone L7.8 specifically bound to N36(L8)C34 and this binding could be blocked by a gp41 core-specific monoclonal antibody (NC-1). JCH-4, a peptide containing HXXNPF motif, effectively inhibited HIV-1 envelope glycoprotein-mediated syncytium-formation. The epitope of JCH-4 was proven to be linear and might locate in the NHR regions of the gp41 core. These data suggest that HXXNPF motif may be a gp41 core-binding sequence and HXXNPF motif-containing molecules can be used as probes for studying the role of the HIV-1 gp41 core in membrane fusion process. [Copyright &y& Elsevier]
- Published
- 2006
- Full Text
- View/download PDF
12. Binding interaction of SARS coronavirus 3CLpro protease with vacuolar-H+ ATPase G1 subunit
- Author
-
Lin, Cheng-Wen, Tsai, Fuu-Jen, Wan, Lei, Lai, Chien-Chen, Lin, Kuan-Hsun, Hsieh, Tsung-Han, Shiu, Shi-Yi, and Li, Jeng-Yi
- Subjects
- *
SARS disease , *ADENOSINE triphosphatase , *HYDROGEN-ion concentration , *LUNGS - Abstract
Abstract: The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is an important issue for treatment and prevention of SARS. Recently, SARS-CoV 3CLpro protease has been implied to be possible relevance to SARS-CoV pathogenesis. In this study, we intended to identify potential 3CLpro-interacting cellular protein(s) using the phage-displayed human lung cDNA library. The vacuolar-H+ ATPase (V-ATPase) G1 subunit that contained a 3CLpro cleavage site-like motif was identified as a 3CLpro-interacting protein, as confirmed using the co-immunoprecipitation assay and the relative affinity assay. In addition, our result also demonstrated the cleavage of the V-ATPase G1 fusion protein and the immunoprecipitation of cellular V-ATPase G1 by the 3CLpro. Moreover, loading cells with SNARF-1 pH-sensitive dye showed that the intracellular pH in 3CLpro-expressing cells was significantly lower as compared to mock cells. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
13. A bifunctional Gαi/Gαs modulatory peptide that attenuates adenylyl cyclase activity
- Author
-
Johnston, Christopher A., Ramer, J. Kevin, Blaesius, Rainer, Fredericks, Zoey, Watts, Val J., and Siderovski, David P.
- Subjects
- *
ADENYLATE cyclase , *BIOSENSORS , *MICROBIAL genetics , *CYCLIC adenylic acid - Abstract
Abstract: Signaling via G-protein coupled receptors is initiated by receptor-catalyzed nucleotide exchange on Gα subunits normally bound to GDP and Gβγ. Activated Gα·GTP then regulates effectors such as adenylyl cyclase. Except for Gβγ, no known regulators bind the adenylyl cyclase-stimulatory subunit Gαs in its GDP-bound state. We recently described a peptide, KB-752, that binds and enhances the nucleotide exchange rate of the adenylyl cyclase-inhibitory subunit Gαi. Herein, we report that KB-752 binds Gαs ·GDP yet slows its rate of nucleotide exchange. KB-752 inhibits GTPγS-stimulated adenylyl cyclase activity in cell membranes, reflecting its opposing effects on nucleotide exchange by Gαi and Gαs. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
14. Cry11Aa toxin from Bacillus thuringiensis binds its receptor in Aedes aegypti mosquito larvae through loop α-8 of domain II
- Author
-
Fernández, Luisa E., Pérez, Claudia, Segovia, Lorenzo, Rodríguez, Mario H., Gill, Sarjeet S., Bravo, Alejandra, and Soberón, Mario
- Subjects
- *
BACILLUS thuringiensis , *TOXINS , *DEVELOPMENTAL biology , *EPITHELIAL cells - Abstract
Abstract: Bacillus thuringiensis subs israelensis produces Cry toxins active against mosquitoes. Receptor binding is a key determinant for specificity of Cry toxins composed of three domains. We found that exposed loop α-8 of Cry11Aa toxin, located in domain II, is an important epitope involved in receptor interaction. Synthetic peptides corresponding to exposed regions in domain II (loop α-8, β-4 and loop 3) competed binding of Cry11Aa to membrane vesicles from Aedes aegypti midgut microvilli. The role of loop α-8 of Cry11A in receptor interaction was demonstrated by phage display and site-directed mutagenesis. We isolated a peptide-displaying phage (P5.tox), that recognizes loop α-8 in Cry11Aa, interferes interaction with the midgut receptor and attenuates toxicity in bioassay. Loop α-8 mutants affected in toxicity and receptor binding were characterized. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
15. An antibody library for stabilizing and crystallizing membrane proteins – selecting binders to the citrate carrier CitS
- Author
-
Röthlisberger, Daniela, Pos, Klaas Martinus, and Plückthun, Andreas
- Subjects
- *
MEMBRANE proteins , *CRYSTALLIZATION , *IMMUNOGLOBULINS , *CRYSTAL growth - Abstract
Co-crystallization of membrane proteins with antibody fragments may emerge as a general tool to facilitate crystal growth and improve crystal quality. The bound antibody fragment enlarges the hydrophilic part of the mostly hydrophobic membrane protein, thereby increasing the interaction area for possible protein–protein contacts in the crystal. Additionally, it may restrain flexible parts or lock the membrane protein in a defined conformational state. For successful co-crystallization trials, the antibody fragments must be stable in detergents during the extended period of crystal growth and must be easily produced in amounts necessary for crystallography. Therefore, we constructed a library of antibody Fab fragments from a framework subset of the HuCAL GOLD® library (Morphosys, Munich, Germany). By combining the most stable and well expressed frameworks, VH3 and Vκ3, with the further stabilizing constant domains, a Fab library with the desired properties was obtained in a standard phage display format. As a proof of principle, we selected binders with phage display against the detergent-solubilized citrate transporter CitS of Klebsiella pneumoniae. We describe efficient methods for the immobilization of the membrane protein during selection, for ELISA screening, and for BIAcore evaluation. We demonstrate that the selected Fab fragments form stable complexes with native CitS and recognize conformational epitopes with affinities in the low nanomolar range. [Copyright &y& Elsevier]
- Published
- 2004
- Full Text
- View/download PDF
16. A new member of the bacterial ribonuclease inhibitor family from Saccharopolyspora erythraea
- Author
-
Krajcikova, Daniela and Hartley, Robert W.
- Subjects
- *
RIBONUCLEASES , *MESSENGER RNA , *GENE libraries , *STREPTOMYCES - Abstract
We have identified Sti, the gene of a ribonuclease inhibitor from Saccharopolyspora erythraea, by using a T7 phage display system. A specific phage has been isolated from a genome library by a biopanning procedure, using RNase Sa3, a ribonuclease from Streptomyces aureofaciens, as bait. Sti, a protein of 121 amino acid residues, with molecular mass 13 059 Da, is a homolog of barstar and other microbial ribonuclease inhibitors. To overexpress its gene in Escherichia coli, we optimized the secondary structure of its mRNA by introducing a series of silent mutations. Soluble protein was isolated and purified to homogeneity. Inhibition constants of complex of Sti and RNase Sa3 or barnase were determined at pH 7 as 5×10−12 or 7×10−7, respectively. [Copyright &y& Elsevier]
- Published
- 2004
- Full Text
- View/download PDF
17. Selection and characterisation of binders based on homodimerisation of immunoglobulin VH domains
- Author
-
Jin, Hulin, Sepúlveda, Jorge, and Burrone, Oscar R.
- Subjects
- *
ANTIGENS , *IMMUNOGLOBULINS , *DIMERS - Abstract
The antigen-binding surface of antibodies is formed by the heterodimerisation of the two variable domains of the light (VL) and heavy (VH) chains. We have previously described the spontaneous formation of VH dimers (VHD) in both bacteria and mammalian cells. The self-association of a single domain produces a homo-VHD, in which the two identical VH domains generate a unique symmetric surface for antigen binding that is never found in the normal VL/VH antibody binding site. We developed a phagemid vector for the construction of phage display libraries in which a cysteine residue, introduced at the C-terminus of the only VH cloned, allowed display of homo-VHDs. Panning of the library on different proteins yielded antigen specific binders against lysozyme, glutathione S-transferase and streptavidin. A lysozyme specific homo-VHD was further characterised with an apparent affinity determined to be 216±6.6 nM. Importantly, the results showed that its binding activity was fully dependent on the dimerisation of both identical VH domains. [Copyright &y& Elsevier]
- Published
- 2003
- Full Text
- View/download PDF
18. VirB6 and VirB10 from theBrucellatype IV secretion system interact via the N-terminal periplasmic domain of VirB6
- Author
-
Ana Maria Villamil Giraldo, Christian Baron, Charline Mary, and Durgajini Sivanesan
- Subjects
Phage display ,Green Fluorescent Proteins ,Molecular Sequence Data ,Biophysics ,Biology ,Biochemistry ,Protein–protein interaction ,Bacterial Proteins ,Structural Biology ,Two-Hybrid System Techniques ,Genetics ,Inner membrane ,Bacteriophages ,Secretion ,Amino Acid Sequence ,Molecular Biology ,Binding Sites ,Cell Biology ,Periplasmic space ,Brucella ,Cell biology ,Bacterial virulence ,A-site ,Spectrometry, Fluorescence ,Type IV secretion system ,Membrane protein ,Periplasm ,Cell envelope - Abstract
Type IV secretion systems are multi-protein complexes that transfer macromolecules across the cell envelope of bacteria. Identifying the sites of interaction between the twelve proteins (VirB1–VirB11 and VirD4) that form these complexes is key to understanding their assembly and function. We have here used phage display, bacterial two-hybrid and fluorescence-based interaction assays to identify an N-terminal domain of the inner membrane protein VirB6 as a site of interaction with the envelope-spanning VirB10 protein. Our results are consistent with the notion that VirB6 acts in concert with VirB10 as well as with VirB8 during secretion system assembly and function.
- Published
- 2015
- Full Text
- View/download PDF
19. Conformation‐dependent single‐chain variable fragment antibodies specifically recognize beta‐amyloid oligomers
- Author
-
William L. Klein, Shi gao Yang, Xue ting Du, Ying Feng, Mary P. Lambert, Yu jiong Wang, Jun hua Zhang, Xi Zhang, Rui-tian Liu, Xiao-xia Sun, Min Zhao, Ji-Liang Li, and Xiao ping Wang
- Subjects
Amyloid ,Phage display ,Cell Survival ,Biophysics ,chemical and pharmacologic phenomena ,Beta-amyloid ,Fibril ,Biochemistry ,Oligomer ,Antibodies ,Epitope ,Epitopes ,chemistry.chemical_compound ,Single-chain variable fragment ,Antibody Specificity ,Structural Biology ,Cell Line, Tumor ,Genetics ,Humans ,Cytotoxicity ,Molecular Biology ,Chemistry ,Cell Biology ,respiratory system ,Kinetics ,Monomer ,Protein Multimerization ,Alzheimer’s disease ,Protein Binding - Abstract
Increasing evidence indicates that beta-amyloid (Abeta) oligomers rather than monomers or fibrils are the major toxic agents that specifically inhibit synaptic plasticity and long-term potentiation (LTP) in Alzheimer's disease (AD). Neutralization of Abeta oligomeric toxicity was found to reverse memory deficits. Here, we report four single-chain variable fragment (scFv) antibodies isolated from the naive human scFv library by phage display that specifically recognized Abeta oligomers but not monomers and fibrils. These conformation-dependent scFv antibodies inhibit both Abeta fibrillation and cytotoxicity and bind to the same type of eptitope displayed on the Abeta oligomers. Such scFv antibodies specifically targeting toxic Abeta oligomers may have potential therapeutic and diagnostic applications for AD.
- Published
- 2009
- Full Text
- View/download PDF
20. An antibody library for stabilizing and crystallizing membrane proteins - selecting binders to the citrate carrier CitS
- Author
-
Andreas Plückthun, Daniela Röthlisberger, Klaas M. Pos, University of Zurich, and Plückthun, A
- Subjects
1303 Biochemistry ,Phage display ,Protein Conformation ,Biophysics ,Enzyme-Linked Immunosorbent Assay ,Biochemistry ,Horseradish peroxidase ,Epitope ,1307 Cell Biology ,Immunoglobulin Fab Fragments ,1315 Structural Biology ,1311 Genetics ,Bacterial Proteins ,Peptide Library ,Structural Biology ,10019 Department of Biochemistry ,1312 Molecular Biology ,Genetics ,Bovine serum albumin ,Molecular Biology ,biology ,Chemistry ,Membrane Proteins ,Cell Biology ,Antibody library ,Combinatorial chemistry ,Affinities ,Dissociation constant ,Klebsiella pneumoniae ,Membrane protein ,biology.protein ,570 Life sciences ,Antibody ,Carrier Proteins ,Crystallization ,Co-crystallization ,1304 Biophysics ,Protein Binding - Abstract
Co-crystallization of membrane proteins with antibody fragments may emerge as a general tool to facilitate crystal growth and improve crystal quality. The bound antibody fragment enlarges the hydrophilic part of the mostly hydrophobic membrane protein, thereby increasing the interaction area for possible protein–protein contacts in the crystal. Additionally, it may restrain flexible parts or lock the membrane protein in a defined conformational state. For successful co-crystallization trials, the antibody fragments must be stable in detergents during the extended period of crystal growth and must be easily produced in amounts necessary for crystallography. Therefore, we constructed a library of antibody Fab fragments from a framework subset of the HuCAL GOLD® library (Morphosys, Munich, Germany). By combining the most stable and well expressed frameworks, VH3 and Vκ3, with the further stabilizing constant domains, a Fab library with the desired properties was obtained in a standard phage display format. As a proof of principle, we selected binders with phage display against the detergent-solubilized citrate transporter CitS of Klebsiella pneumoniae. We describe efficient methods for the immobilization of the membrane protein during selection, for ELISA screening, and for BIAcore evaluation. We demonstrate that the selected Fab fragments form stable complexes with native CitS and recognize conformational epitopes with affinities in the low nanomolar range.
- Published
- 2004
- Full Text
- View/download PDF
21. A new member of the bacterial ribonuclease inhibitor family fromSaccharopolyspora erythraea
- Author
-
Robert W. Hartley and Daniela Krajcikova
- Subjects
Phage display ,RNase P ,Ribonuclease inhibitor ,Molecular Sequence Data ,Biophysics ,Streptomyces aureofaciens ,Polymerase Chain Reaction ,Biochemistry ,Ribonuclease ,mRNA secondary structure ,Ribonucleases ,Bacterial Proteins ,Structural Biology ,Escherichia coli ,Genetics ,Amino Acid Sequence ,RNA, Messenger ,Cloning, Molecular ,Enzyme Inhibitors ,Molecular Biology ,DNA Primers ,Barnase ,Genomic Library ,Base Sequence ,Sequence Homology, Amino Acid ,biology ,Cell Biology ,biology.organism_classification ,Molecular biology ,Kinetics ,Barstar ,Mutagenesis ,biology.protein ,Saccharopolyspora erythraea ,Sequence Alignment ,Saccharopolyspora - Abstract
We have identified Sti, the gene of a ribonuclease inhibitor from Saccharopolyspora erythraea, by using a T7 phage display system. A specific phage has been isolated from a genome library by a biopanning procedure, using RNase Sa3, a ribonuclease from Streptomyces aureofaciens, as bait. Sti, a protein of 121 amino acid residues, with molecular mass 13 059 Da, is a homolog of barstar and other microbial ribonuclease inhibitors. To overexpress its gene in Escherichia coli, we optimized the secondary structure of its mRNA by introducing a series of silent mutations. Soluble protein was isolated and purified to homogeneity. Inhibition constants of complex of Sti and RNase Sa3 or barnase were determined at pH 7 as 5×10−12 or 7×10−7, respectively.
- Published
- 2003
- Full Text
- View/download PDF
22. A novel grass pollen allergen mimotope identified by phage display peptide library inhibits allergen-human IgE antibody interaction
- Author
-
George F. Schäppi, Janet M. Davies, Robyn E O'Hehir, J. Kenrick, David Levy, and Cenk Suphioglu
- Subjects
Phage display ,medicine.drug_class ,Immunoblotting ,Biophysics ,Enzyme-Linked Immunosorbent Assay ,Peptide ,Biopanning ,Biology ,Poaceae ,Monoclonal antibody ,Biochemistry ,Epitope ,Mice ,Peptide Library ,Structural Biology ,otorhinolaryngologic diseases ,Genetics ,medicine ,Animals ,Humans ,Peptide library ,Molecular Biology ,chemistry.chemical_classification ,Mice, Inbred BALB C ,Mimotope ,Allergen ,Human immunoglobulin E ,Grass pollen ,Antibodies, Monoclonal ,food and beverages ,Cell Biology ,Allergens ,Immunoglobulin E ,Molecular biology ,chemistry ,Antiallergic agent ,Epitopes, B-Lymphocyte ,Pollen ,Peptides ,Sequence Analysis - Abstract
The aim of this study was to investigate the molecular basis of human IgE–allergen interaction by screening a phage-displayed peptide library with an allergen-specific human IgE-mimicking monoclonal antibody (mAb). A mAb that reacted with major grass pollen allergens was successfully identified and shown to inhibit human IgE–allergen interaction. Biopanning of a phage-displayed random peptide library with this mAb yielded a 12 amino acid long mimotope. A synthetic peptide based on this 12-mer mimotope inhibited mAb and human IgE binding to grass pollen extracts. Our results indicate that such synthetic peptide mimotopes of allergens have potential as novel therapeutic agents.
- Published
- 2001
- Full Text
- View/download PDF
23. Homing markers for atherosclerosis: applications for drug delivery, gene delivery and vascular imaging
- Author
-
Martin Braddock, Parul Houston, Jo Goodman, Alan Lewis, and Callum J. Campbell
- Subjects
Phage display ,Arteriosclerosis ,Biophysics ,Biopanning ,Gene delivery ,Biology ,Kidney ,Binding, Competitive ,Biochemistry ,Mice ,Drug Delivery Systems ,Peptide Library ,Sequence Analysis, Protein ,Structural Biology ,Genetics ,medicine ,Animals ,Bacteriophages ,Endothelial dysfunction ,Molecular Biology ,Mice, Knockout ,Binding Sites ,Gene Transfer Techniques ,Homing markers ,Arteries ,Cell Biology ,Atherosclerosis ,medicine.disease ,Disease Models, Animal ,Receptors, LDL ,Organ Specificity ,Drug delivery ,LDL receptor ,Immunology ,Knockout mouse ,Cancer research ,Peptides ,Vascular imaging - Abstract
Endothelial dysfunction plays a major role in the pathogenesis of atherosclerosis. Pro-inflammatory cytokines such as interleukin-1β and tumour necrosis factor α activate endothelial cells changing their resting phenotype to become pro-adhesive, pro-thrombotic and pro-atherogenic. Phage display in vivo biopanning has been used to identify peptide sequences that home to diseased regions of the vessel wall in low density lipoprotein receptor (LDLr) knockout mice. In LDLr knockout mice, peptide sequence determinants exhibiting organ specificity have been isolated. These sequences have applications for gene delivery, drug delivery and for improving contrast agents for vascular imaging.
- Published
- 2001
- Full Text
- View/download PDF
24. Convergent evolution with combinatorial peptides
- Author
-
Jeremy Kasanov, Alexei Kurakin, Brian K. Kay, and Stephen M.G Knight
- Subjects
Phage display ,Proteome ,Molecular Sequence Data ,PDZ domain ,Biophysics ,Computational biology ,Biology ,Ligands ,EH domain ,Biochemistry ,SH3 domain ,Protein–protein interaction ,Evolution, Molecular ,WW domain ,Peptide Library ,Structural Biology ,Interaction network ,Molecular evolution ,Darwinian evolution ,Genetics ,Animals ,Combinatorial Chemistry Techniques ,Humans ,Estrogen receptor ,Amino Acid Sequence ,Molecular Biology ,Binding Sites ,Protein interaction module ,Proteins ,Cell Biology ,Protein Structure, Tertiary ,biology.protein ,Phage-display ,Target protein ,Function (biology) ,Protein Binding - Abstract
Once the sequence of a genome is in hand, understanding the function of its encoded proteins becomes a task of paramount importance. Much like the biochemists who first outlined different biochemical pathways, many genomic scientists are engaged in determining which proteins interact with which proteins, thereby establishing a protein interaction network. While these interactions have evolved in regard to their specificity, affinity and cellular function over billions of years, it is possible in the laboratory to isolate peptides from combinatorial libraries that bind to the same proteins with similar specificity, affinity and primary structures, which resemble those of the natural interacting proteins. We have termed this phenomenon ‘convergent evolution’. In this review, we highlight various examples of convergent evolution that have been uncovered in experiments dissecting protein–protein interactions with combinatorial peptides. Thus, a fruitful approach for mapping protein–protein interactions is to isolate peptide ligands to a target protein and identify candidate interacting proteins in a sequenced genome by computer analysis.
- Published
- 2000
- Full Text
- View/download PDF
25. Contribution of the different modules in the utrophin carboxy-terminal region to the formation and regulation of the DAP complex
- Author
-
Giovanni Di Zenzo, Marius Sudol, Alice Tommasi di Vignano, Gianni Cesareni, and Luciana Dente
- Subjects
Phage display ,Utrophin ,Calmodulin ,Recombinant Fusion Proteins ,Biophysics ,Muscle Proteins ,DRP2 ,Biology ,Ligands ,Binding, Competitive ,Biochemistry ,Substrate Specificity ,Dystrophin ,Peptide Library ,Structural Biology ,Consensus Sequence ,Genetics ,Humans ,Amino Acid Sequence ,EF Hand Motifs ,Dystroglycans ,Peptide library ,Molecular Biology ,Gene ,Sequence Deletion ,Dystrophin-associated protein ,Membrane Glycoproteins ,Neuropeptides ,Membrane Proteins ,Cell Biology ,Protein superfamily ,musculoskeletal system ,Peptide Fragments ,Modular domain ,Protein Structure, Tertiary ,Cell biology ,Cytoskeletal Proteins ,Amino Acid Substitution ,Dystrophin-Associated Proteins ,biology.protein ,Calcium ,Dimerization ,Protein Binding - Abstract
The carboxy-terminal region of utrophin, like the homologous proteins dystrophin, Drp2 and dystrobrevins, contains structural domains frequently involved in protein-protein interaction. These domains (WW, EF hands, ZZ and H1-H2) mediate recognition and binding to a multicomponent complex of proteins, also known as dystrophin-associated proteins (DAPs) for their association with dystrophin, the product of the gene, mutated in Duchenne muscular dystrophy. We have exploited phage display and in vitro binding assays to study the recognition specificity of the different domains of the utrophin carboxy-terminus. We found that none of the carboxy-terminal domains of utrophin, when isolated from its structural context, selects specific ligand peptides from a phage-displayed peptide library. By contrast, panning with an extended region containing the WW, EF hands, and ZZ domain defines the consensus binding motif, PPxY which is also found in beta-dystroglycan, a component of the DAP complex that interacts with utrophin in several tissues. WW-mediated binding to PPxY peptides and to beta-dystroglycan requires the presence of the EF hands and ZZ domain. When the ZZ domain is either deleted or engaged in binding to calmodulin, the utrophin beta-dystroglycan complex cannot be formed. These findings suggest a potential regulatory mechanism by means of which the attachment of utrophin to the DAP complex can be modulated by the Ca(2+)-dependent binding of calmodulin. The remaining two motifs found in the carboxy-terminus (H1-H2) mediate the formation of utrophin-dystrobrevin hybrids but do not select ligands in a repertoire of random nonapeptides.
- Published
- 2000
- Full Text
- View/download PDF
26. Selection of phage-displayed Fab antibodies on the active conformation of Ras yields a high affinity conformation-specific antibody preventing the binding of c-Raf kinase to Ras
- Author
-
Hennie R. Hoogenboom, Alfred Wittinghofer, Ivo R. Horn, and Adriaan P. de Bruïne
- Subjects
Time Factors ,Phage display ,Protein Conformation ,Biophysics ,Surface plasmon resonance analysis ,Enzyme-Linked Immunosorbent Assay ,GTPase ,Binding, Competitive ,Guanosine Diphosphate ,Biochemistry ,Ras conformation ,Antibodies ,SH3 domain ,GTP Phosphohydrolases ,Immunoglobulin Fab Fragments ,Anti-GTP-Ras antibody ,GTPase activity ,Antibody Specificity ,Peptide Library ,Structural Biology ,Genetics ,Humans ,c-Raf ,Binding site ,Molecular Biology ,c-Raf kinase ,biology ,Kinase ,Chemistry ,Cell Biology ,Surface Plasmon Resonance ,Antibody selection ,Molecular biology ,In vitro ,Proto-Oncogene Proteins c-raf ,ras Proteins ,biology.protein ,Antibody ,Epitope Mapping ,Protein Binding - Abstract
The Ras proteins cycle in the cell between an inactive state and an active state. In the active state, Ras signals via the switch I region to effectors like c-Raf kinase, leading to cell growth. Since Ras mutations in cancer are often associated with the presence of permanently active Ras, molecules that prevent downstream signaling may be of interest. Here, we show that by selection on the active conformation of Ras, using a recently described large phage antibody repertoire [de Haard et al. (1999) J. Biol. Chem. 274, 18218–18230], a Fab antibody (Fab H2) was identified that exclusively binds to active Ras, and not to inactive Ras. Using surface plasmon resonance (SPR) analysis, the interaction was demonstrated to be of high affinity (7.2 nM). In addition, the interaction with Ras is specific, since binding to the homologous Rap1A protein in BIAcore analysis is at least three orders of magnitude lower, and undetectable in an enzyme-linked immunosorbent assay. The antibody fragment prevents the binding of active Ras to the immobilized Ras-binding domain of c-Raf kinase (Raf-RBD) at an IC50 value of 135 nM. This value compares well to the KD of active Ras-binding to immobilized Raf-RBD using SPR, suggesting identical binding sites. Like the IgG Y13-259, which does not demonstrate preferential binding to either inactive or active Ras, Fab H2 inhibits intrinsic GTPase activity of Ras in vitro. Mapping studies using SPR analysis demonstrate that the binding sites for the antibodies are non-identical. This antibody could be used for dissecting functional differences between Ras effectors. Due to its specificity for active Ras, Fab H2 may well be more selective than previously used anti-Ras antibodies, and thus could be used for gene therapy of cancer with intracellular antibodies.
- Published
- 1999
- Full Text
- View/download PDF
27. Structural analysis of a plant sucrose carrier using monoclonal antibodies and bacteriophage lambda surface display
- Author
-
Ju º rgen Stolz, Klaus Hagemann, Ruth Stadler, Norbert Sauer, Christian Biesgen, and Andreas Ludwig
- Subjects
Monoclonal antibody ,Cytoplasm ,Sucrose ,Phage display ,Sucrose transport ,Protein Conformation ,medicine.drug_class ,Molecular Sequence Data ,Biophysics ,Topology ,Biochemistry ,Epitope ,Antibody Specificity ,Peptide Library ,Structural Biology ,Genetics ,medicine ,Amino Acid Sequence ,skin and connective tissue diseases ,Plantago ,Molecular Biology ,Peptide sequence ,Plant Proteins ,Plants, Medicinal ,biology ,Membrane transport protein ,Chemistry ,Cell Membrane ,Antibodies, Monoclonal ,Cell Polarity ,Membrane Transport Proteins ,Biological Transport ,Cell Biology ,Bacteriophage lambda ,Molecular biology ,Recombinant Proteins ,Transmembrane domain ,Epitope mapping ,biology.protein ,Carrier Proteins ,Epitope Mapping ,hormones, hormone substitutes, and hormone antagonists - Abstract
Monoclonal antibodies were raised and selected against recombinant Plantago major PmSUC2 sucrose carrier protein. Epitopes of two monoclonal antibodies (PS2-1A2 and PS2-4D4) were mapped using N-terminally truncated PmSUC2 proteins and a lambda library displaying random PmSUC2 peptides. PS2-1A2 recognizes an octapeptide close to the N-terminus of PmSUC2, PS2-4D4 binds to a decapeptide at the very C-terminus. Analyses of antibody binding to yeast protoplasts with functionally active, tagged PmSUC2 protein revealed that both epitopes are located in cytoplasmic domains of PmSUC2. These results support a model for plant sucrose transporters containing 12 transmembrane helices with the N-terminus and the C-terminus on the cytoplasmic side of the plasma membrane.
- Published
- 1999
- Full Text
- View/download PDF
28. Selection of peptides that bind to plasminogen activator inhibitor 1 (PAI-1) using random peptide phage-display libraries
- Author
-
Anton Jan van Zonneveld, Hans Pannekoek, Henrik Gårdsvoll, Eric Eldering, Keld Danø, Arne Holm, Marja van Meijer, and Other departments
- Subjects
Phage display ,Concatemer ,Phagemid ,Molecular Sequence Data ,Biophysics ,Peptide ,Biochemistry ,chemistry.chemical_compound ,Structural Biology ,Genetics ,Humans ,Bacteriophages ,Amino Acid Sequence ,Plasminogen activator inhibitor 1 ,Peptide library ,Molecular Biology ,Peptide sequence ,Serine protease ,chemistry.chemical_classification ,Binding Sites ,Sequence Homology, Amino Acid ,biology ,Chemistry ,Cell Biology ,Urokinase-Type Plasminogen Activator ,Molecular biology ,Plasminogen activator inhibitor-1 ,biology.protein ,Peptides - Abstract
Large random hexa- and decapenta-peptide libraries were constructed and displayed on the surface of the filamentous phagemid pComb8. Panning of the hexa-peptide library on immobilized plasminogen activator inhibitor 1 (PAI-1) specifically selected a minor fraction of concatemers, indicating that binding to PAI-1 requires an extended amino acid sequence. Accordingly, the decapenta-peptide library exclusively yielded PAI-1 binding peptides of 15 amino acid residues. None of these phage-bound peptides prevented the interaction between PAI-1 and its target serine protease urokinase (u-PA). To isolate peptides that block the interaction between PAI-1 and u-PA, phages bound to immobilized PAI-1 were eluted by incubation with u-PA. Remarkably, this procedure resulted in elution of a unique phage type that harbors a concatemer of decapentamers, consisting of 49 amino acid residues with no obvious similarity to the primary sequence of PAI-1 or u-PA.
- Published
- 1998
- Full Text
- View/download PDF
29. Epitope mapping by screening of phage display libraries of a monoclonal antibody directed against the receptor binding domain of human α2-macroglobulin
- Author
-
Thomas Mothes, Gerd Birkenmeier, Gerhard Kopperschläger, and Awad A. Osman
- Subjects
Monoclonal antibody ,Phage display ,Protein Conformation ,medicine.drug_class ,Epitope mapping ,Molecular Sequence Data ,Biophysics ,Peptide ,Binding, Competitive ,Biochemistry ,Epitope ,Epitopes ,Phage display library ,Peptide Library ,Structural Biology ,α2-Macroglobulin ,Genetics ,medicine ,Animals ,Humans ,alpha-Macroglobulins ,Amino Acid Sequence ,Receptors, Immunologic ,Molecular Biology ,chemistry.chemical_classification ,Binding Sites ,Sequence Homology, Amino Acid ,biology ,Mimotope ,Antibodies, Monoclonal ,Cell Biology ,Molecular biology ,Macroglobulin ,Models, Structural ,Molecular Weight ,Kinetics ,chemistry ,biology.protein ,Cattle ,Antibody ,Sequence Alignment ,Low Density Lipoprotein Receptor-Related Protein-1 - Abstract
The human proteinase inhibitor, alpha2-macroglobulin (a2-M), inhibits a large number of proteinases. Alpha2-M-proteinase complexes are rapidly cleared from the circulation by binding to a cellular receptor (alpha2-M-R/LRP) via the receptor binding domain (RBD) which is made up of a 20 kDa C-terminal stretch of the 180 kDa monomer of the inhibitor. A monoclonal antibody (mab alpha-1) has been described which reacts with the receptor-recognizable form of the inhibitor, the so called transformed alpha2-M (a2-Mt). By screening of a phage display library an epitope in the RBD of the inhibitor was identified that reacts with mab alpha-1. Out of 25 phage clones a heptapeptide sequence (S-x1-x2-D-x3-x4-K) was obtained containing identical amino acids in three positions. A consensus peptide (S-R-S-D-P-P-K) was synthesized and found to displace alpha2-Mt from binding to mab alpha-1 and to receptor. The specificity of competition was demonstrated by a reversed peptide and a control antibody. By structural comparison it was found that the consensus heptapeptide mimics a discontinuous conformationally constrained epitope present in the RBD of the inhibitor. This is the first report describing the detection of discontinuous epitopes by phage display using a short linear peptide.
- Published
- 1997
- Full Text
- View/download PDF
30. Selection and identification of single domain antibody fragments from camel heavy-chain antibodies
- Author
-
Raymond Hamers, Serge Muyldermans, Aline Desmyter, Lode Wyns, M Arbabi Ghahroudi, Ultrastructure, Cellular and Molecular Immunology, and Vrije Universiteit Brussel
- Subjects
Camelus ,bacteriophages ,binding ,Phage display ,polymerase chain reaction ,binding sites ,domain ,Biophysics ,molecular sequence data ,Single domain antibody fragment ,chain ,Complementarity determining region ,Immunoglobulin light chain ,recombinant proteins ,Biochemistry ,Antibodies ,immunoglobulin heavy chains ,immunology ,cloning, molecular ,antigen ,Structural Biology ,antibody ,camels ,Genetics ,Animals ,gene library ,Panning (camera) ,Molecular Biology ,binding sites, antibody ,Camel ,Heavy-chain antibody ,biology ,Chemistry ,antibody affinity ,antibody specificity ,Cell Biology ,amino acid sequence ,epitope mapping ,Epitope mapping ,Single-domain antibody ,biology.protein ,identification ,Immunoglobulin heavy chain ,light ,protein ,metabolism ,VH - Abstract
Functional heavy-chain γ-immunoglobulins lacking light chains occur naturally in Camelidae. We now show the feasibility of immunising a dromedary, cloning the repertoire of the variable domains of its heavy-chain antibodies and panning, leading to the successful identification of minimum sized antigen binders. The recombinant binders are expressed well in E. coli, extremely stable, highly soluble, and react specifically and with high affinity to the antigens. This approach can be viewed as a general route to obtain small binders with favourable characteristics and valuable perspectives as modular building blocks to manufacture multispecific or multifunctional chimaeric proteins.
- Published
- 1997
- Full Text
- View/download PDF
31. Mutations in B-type natriuretic peptide mediating receptor-A selectivity
- Author
-
Jill Schoenfeld, David G. Lowe, and Jeff Y.K. Tom
- Subjects
Natriuretic peptide receptor ,medicine.medical_specialty ,Phage display ,medicine.drug_class ,Receptor/hormone interaction ,Molecular Sequence Data ,Biophysics ,Transfection ,medicine.disease_cause ,Binding, Competitive ,Polymerase Chain Reaction ,Biochemistry ,Cell Line ,Substrate Specificity ,Atrial natriuretic peptide ,Structural Biology ,Internal medicine ,Natriuretic Peptide, Brain ,Genetics ,medicine ,Natriuretic peptide ,Humans ,Amino Acid Sequence ,Receptor ,Cyclic GMP ,Molecular Biology ,Peptide sequence ,DNA Primers ,Gene Library ,Mutation ,Base Sequence ,Chemistry ,Genetic Variation ,Cell Biology ,NPR1 ,Molecular biology ,NPR2 ,Recombinant Proteins ,Kinetics ,Endocrinology ,Guanylate Cyclase ,B-type natriuretic peptide ,Mutagenesis ,Mutagenesis, Site-Directed ,Receptors, Atrial Natriuretic Factor ,Sequence Alignment ,Atrial Natriuretic Factor - Abstract
Libraries of monovalent display-phage expressing mutant human B-type natriuretic peptide (hBNP) were used to identify variants that preferentially bind natriuretic peptide receptor-A (NPR-A) compared to receptor-C (NPR-C). Position 19 was a significant determinant of receptor specificity for hBNP display phage. The synthetic hBNP variant S19R had a 265-fold improved NPR-A binding over NPR-C, analogous to the atrial natriuretic peptide (ANP) specificity mutation G16R. Mutation of the last three residues of the hBNP disulfide ring, G23F/L24W/G25R, resulted in about 9-fold improved selectivity. The analogous mutations in ANP decreased NPR-A binding, suggesting divergence in the mechanism of NPR-A recognition.
- Published
- 1997
- Full Text
- View/download PDF
32. Development of inhibitors in the ubiquitination cascade
- Author
-
Wei Zhang and Sachdev S. Sidhu
- Subjects
Proteasome Endopeptidase Complex ,Biophysics ,Cancer therapy ,Biochemistry ,Article ,Small Molecule Libraries ,Ubiquitin ,Structural Biology ,Ubiquitin variant (Ubv) ,Drug Discovery ,Genetics ,Animals ,Humans ,Molecular Biology ,Ubiquitins ,biology ,Mechanism (biology) ,Drug discovery ,Ubiquitination ,Cell Biology ,Protein engineering ,3. Good health ,Cell biology ,Proteasome ,biology.protein ,Deubiquitinating enzyme (DUB) ,Phage display ,Neuroscience ,Proteasome Inhibitors ,Small molecule - Abstract
The ubiquitin proteasome system (UPS) is essential in regulating myriad aspects of protein functions. It is therefore a fundamentally important regulatory mechanism that impacts most if not all aspects of cellular processes. Indeed, malfunction of UPS components is implicated in human diseases such as neurodegenerative and immunological disorders and many cancers. The success of proteasome inhibitors in cancer therapy suggests that modulating enzymes in the ubiquitination cascade would be clinically important for therapeutic benefits. In this review, we summarize advances in developing inhibitors of a variety of UPS components. In particular, we highlight recent work done on the protein engineering of ubiquitin as modulators of the UPS, a novel approach that may shed light on innovative drug discovery in the future.
- Published
- 2013
33. Preferential recognition of the very low-density lipoprotein receptor ligand binding site by antibodies from phage display libraries
- Author
-
Dieter Blaas, Doris M. Pfistermueller, and Regina A. Hodits
- Subjects
Phage display ,Rhinovirus ,Molecular Sequence Data ,Immunoglobulin Variable Region ,Biophysics ,Very Low-Density Lipoprotein Receptor ,Receptors, Cell Surface ,Binding, Competitive ,Biochemistry ,Antibody fragments ,Epitopes ,Vitellogenin ,Structural Biology ,Genetics ,Single chain antibody ,Animals ,Humans ,Bacteriophages ,Amino Acid Sequence ,Cloning, Molecular ,LDL-Receptor Related Protein-Associated Protein ,Receptor ,Molecular Biology ,Gene Library ,Glycoproteins ,biology ,Immune Sera ,Egg Proteins ,Very low-density lipoprotein receptor ,Cell Biology ,Molecular biology ,In vitro ,Receptors, LDL ,biology.protein ,Calcium ,Rabbits ,Antibody ,Carrier Proteins ,Lipoprotein - Abstract
Screening of a phage library displaying single chain fragments of the variable regions of human immunoglobulins (scFv) for binding to the ovarian chicken very low-density lipoprotein/vitellogenin receptor (OVR) led to the isolation of several antibody fragments with high affinity. As for the natural ligands of OVR, receptor binding of all antibody fragments is strictly Ca2+-dependent and is prevented by receptor-associated protein (RAP). Moreover, attachment of human rhinovirus serotype 2 (HRV2) to this receptor is inhibited by all scFvs. In contrast to conventional immunization, the in vitro selection method thus exclusively led to antibodies that attach to or close to the ligand binding site and thereby block the receptor-ligand interaction.
- Published
- 1996
- Full Text
- View/download PDF
34. Antibodies for all: The case for genome-wide affinity reagents
- Author
-
Sachdev S. Sidhu
- Subjects
Biophysics ,Nanotechnology ,Biochemistry ,Genome ,Antibodies ,src Homology Domains ,Affinity Reagent ,Structural Biology ,Basic research ,Peptide Library ,Research community ,Protein Interaction Mapping ,Genetics ,Animals ,Humans ,Molecular Biology ,Genome, Human ,Systems Biology ,Cell Biology ,Data science ,Cultural shift ,Affinity reagents ,Protein Structure, Tertiary ,Domains ,Indicators and Reagents ,Business ,Phage display ,Networks ,Genome-Wide Association Study ,Protein Binding - Abstract
For more than 30years, the production of research antibodies has been dominated by hybridoma technologies, while modern recombinant technologies have lagged behind. Here I discuss why this situation must change if we are to generate reliable, comprehensive reagent sets on a genome-wide scale, and I describe how a cultural shift in the research community could revolutionize and modernize the affinity reagent field. In turn, such a revolution would pay huge dividends by closing the gap between basic research and therapeutic development, thus enabling the development of myriad new therapies for unmet medical needs.
- Published
- 2012
35. A bifunctional Galphai/Galphas modulatory peptide that attenuates adenylyl cyclase activity
- Author
-
Rainer Blaesius, J. Kevin Ramer, Val J. Watts, Zoey Fredericks, David P. Siderovski, and Christopher A. Johnston
- Subjects
Gs alpha subunit ,Biophysics ,GTP-Binding Protein alpha Subunits, Gi-Go ,Biochemistry ,Adenylyl Cyclase Inhibitors ,ADCY10 ,Article ,Adenylyl cyclase ,03 medical and health sciences ,chemistry.chemical_compound ,Structural Biology ,Surface plasmon resonance ,Genetics ,GTP-Binding Protein alpha Subunits, Gs ,Humans ,heterocyclic compounds ,Molecular Biology ,Cells, Cultured ,030304 developmental biology ,G protein-coupled receptor ,0303 health sciences ,Forskolin ,Chemistry ,030302 biochemistry & molecular biology ,ADCY9 ,Cell Biology ,Cell biology ,enzymes and coenzymes (carbohydrates) ,Biosensors ,G-proteins ,sense organs ,Guanine nucleotide exchange factor ,Phage display ,biological phenomena, cell phenomena, and immunity ,Peptides ,hormones, hormone substitutes, and hormone antagonists ,Signal Transduction - Abstract
Signaling via G-protein coupled receptors is initiated by receptor-catalyzed nucleotide exchange on Galpha subunits normally bound to GDP and Gbetagamma. Activated Galpha . GTP then regulates effectors such as adenylyl cyclase. Except for Gbetagamma, no known regulators bind the adenylyl cyclase-stimulatory subunit Galphas in its GDP-bound state. We recently described a peptide, KB-752, that binds and enhances the nucleotide exchange rate of the adenylyl cyclase-inhibitory subunit Galpha(i). Herein, we report that KB-752 binds Galpha(s) . GDP yet slows its rate of nucleotide exchange. KB-752 inhibits GTPgammaS-stimulated adenylyl cyclase activity in cell membranes, reflecting its opposing effects on nucleotide exchange by Galpha(i) and Galpha(s).
- Published
- 2005
36. Inhibition of the angiogenesis by the MCP-1 (monocyte chemoattractant protein-1) binding peptide
- Author
-
Sunjoo Jeong, Kyung Hee Hong, Ki Hoon Han, Mee Young Kim, and Cheol Woo Byeon
- Subjects
CCR2 ,Phage display ,Angiogenesis ,Receptors, CCR2 ,Biophysics ,Neovascularization, Physiologic ,Peptide ,Angiogenesis Inhibitors ,Biology ,Biochemistry ,Chemokine receptor ,Structural Biology ,Peptide Library ,Genetics ,Animals ,Humans ,CCR10 ,Peptide library ,CCL13 ,Molecular Biology ,Aorta ,Chemokine CCL2 ,chemistry.chemical_classification ,Chemokine receptor 3 ,Chemokine receptor 2 ,Cell Biology ,Surface Plasmon Resonance ,Molecular biology ,Monocyte chemoattractant protein-1 ,Rats ,chemistry ,Chemokine ,Biological Assay ,Receptors, Chemokine ,Oligopeptides - Abstract
The CC chemokine, monocyte chemoattractant protein-1 (MCP-1), plays a crucial role in the initiation of atherosclerosis and has direct effects that promote angiogenesis. To develop a specific inhibitor for MCP-1-induced angiogenesis, we performed in vitro selection employing phage display random peptide libraries. Most of the selected peptides were found to be homologous to the second extracellular loops of CCR2 and CCR3. We synthesized the peptide encoding the homologous sequences of the receptors and tested its effect on the MCP-1 induced angiogenesis. Surface plasmon resonance measurements demonstrated specific binding of the peptide to MCP-1 but not to the other homologous protein, MCP-3. Flow cytometry revealed that the peptide inhibited the MCP-1 binding to THP-1 monocytes. Moreover, CAM and rat aortic ring assays showed that the peptide inhibited MCP-1 induced angiogenesis. Our observations indicate that the MCP-1-binding peptide exerts its anti-angiogenic effect by interfering with the interaction between MCP-1 and its receptor.
- Published
- 2004
37. Binding of phage-display-selected peptides to the periplasmic chaperone protein SurA mimics binding of unfolded outer membrane proteins
- Author
-
David B. McKay and Eduard Bitto
- Subjects
Phage display ,Biophysics ,Enzyme-Linked Immunosorbent Assay ,Cell Biology ,Periplasmic space ,Biology ,Peptidylprolyl Isomerase ,Biochemistry ,Recombinant Proteins ,Survival protein A (SurA) ,Structural Biology ,GST - Glutathione S transferase ,Genetics ,bacteria ,Bacteriophages ,Enzyme-linked immunoabsorbent assay ,Bacterial outer membrane ,Carrier Proteins ,Peptides ,Peptidyl-prolyl isomerase ,Molecular Biology ,Periplasmic molecular chaperone ,Outer membrane protein folding ,Protein Binding - Abstract
SurA is a periplasmic chaperone protein that facilitates maturation of integral outer membrane proteins (OMPs). Short peptides that bind SurA have previously been characterized. In this work, an enzyme-linked immunoabsorbent assay-based competition assay is utilized to demonstrate that binding of such peptides, presented by peptide-tagged phage, mimics binding of biological substrates. Two representative unfolded OMPs, OmpF and OmpG, bind SurA and a core structural fragment thereof in competition with peptide-tagged phage, and with the same order-of-magnitude affinity as the peptides. Additionally, unfolded OmpF and OmpG bind SurA more tightly than an unfolded water-soluble protein, while folded proteins have no measurable affinity, demonstrating a specificity of SurA for OMP polypeptides.
- Published
- 2004
38. Efficient phage display of polypeptides fused to the carboxy-terminus of the M13 gene-3 minor coat protein
- Author
-
Germaine Fuh and Sachdev S. Sidhu
- Subjects
Vascular Endothelial Growth Factor A ,M13 bacteriophage ,Carboxy-terminus ,Phage display ,Phagemid ,Molecular Sequence Data ,Biophysics ,Endothelial Growth Factors ,Coat protein ,Biochemistry ,Structural Biology ,Peptide Library ,Proto-Oncogene Proteins ,Genetics ,mRNA display ,Amino Acid Sequence ,Molecular Biology ,Gene ,Minor coat protein ,Cdna cloning ,Lymphokines ,Binding Sites ,Vascular Endothelial Growth Factor Receptor-1 ,biology ,Vascular Endothelial Growth Factors ,Receptor Protein-Tyrosine Kinases ,Cell Biology ,biology.organism_classification ,Molecular biology ,Artificial Gene Fusion ,DNA-Binding Proteins ,Capsid Proteins ,Peptides ,Linker ,Viral Fusion Proteins ,Bacteriophage M13 - Abstract
We report that, contrary to common belief, polypeptides fused to the carboxy-terminus of the M13 gene-3 minor coat protein are functionally displayed on the phage surface. In a phagemid display system, carboxy-terminal fusion through optimized linker sequences resulted in display levels comparable to those achieved with conventional amino-terminal fusions. These findings are of considerable importance to phage display technology because they enable investigations not suited to amino-terminal display, including the study of protein–protein interactions requiring free carboxy-termini, functional cDNA cloning efforts, and the display of intracellular proteins.
- Published
- 2000
39. Protein stabilization through phage display
- Author
-
Suvobrata Chakravarty, Raghavan Varadarajan, Stefan Dübel, Nivedita Mitra, Iris Queitsch, and Avadhesha Surolia
- Subjects
Protein Denaturation ,Phage display ,RNase P ,Epitope mapping ,Molecular Sequence Data ,Biophysics ,Peptide ,Calorimetry ,In Vitro Techniques ,Fragment complementation ,Biochemistry ,Substrate Specificity ,Ribonucleases ,Structural Biology ,Peptide Library ,Enzyme Stability ,Genetics ,Animals ,Humans ,Amino Acid Sequence ,Molecular Biology ,Conserved Sequence ,DNA Primers ,chemistry.chemical_classification ,Base Sequence ,Sequence Homology, Amino Acid ,Wild type ,Isothermal titration calorimetry ,Cell Biology ,Thermal stability ,Ribonuclease, Pancreatic ,Peptide Fragments ,Complementation ,chemistry ,Mutation ,Thermodynamics ,Protein stabilization - Abstract
RNase S consists of two proteolytic fragments of RNase A, residues 1-20 (S20) and residues 21-124 (S pro). A 15-mer peptide (S15p) with high affinity for S pro was selected from a phage display library. Peptide residues that are buried in the structure of the wild type complex are conserved in S15p though there are several changes at other positions. Isothermal titration calorimetry studies show that the affinity of S15p is comparable to that of the wild type peptide at 25 degrees C. However, the magnitudes of DeltaH(o) and DeltaC(p) are lower for S15p, suggesting that the thermal stability of the complex is enhanced. In agreement with this prediction, at pH 6, the T(m) of the S15p complex was found to be 10 degrees C higher than that of the wild type complex. This suggests that for proteins where fragment complementation systems exist, phage display can be used to find mutations that increase protein thermal stability.
- Published
- 2000
40. Development and application of cytotoxic T lymphocyte-associated antigen 4 as a protein scaffold for the generation of novel binding ligands
- Author
-
Hennie R. Hoogenboom, Twan van den Beuken, Johan Desmet, Erwin Sablon, Nicole Coolen van Neer, and Simon E. Hufton
- Subjects
Protein Folding ,Phage display ,Immunoconjugates ,Integrin ,Biophysics ,Peptide ,chemical and pharmacologic phenomena ,Complementarity determining region ,Immunoglobulin domain ,Ligands ,Biochemistry ,Scaffold ,Abatacept ,Structural Biology ,Antigens, CD ,Genetics ,Cytotoxic T cell ,Humans ,CTLA-4 Antigen ,Receptors, Vitronectin ,Molecular Biology ,Gene Library ,chemistry.chemical_classification ,biology ,hemic and immune systems ,Cell Biology ,Molecular biology ,Antigens, Differentiation ,Amino acid ,Cell biology ,chemistry ,Drug Design ,biology.protein ,Cytotoxic T lymphocyte-associated antigen 4 ,Protein folding ,T-Lymphocytes, Cytotoxic - Abstract
We have explored the possibilities of using human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) as a single immunoglobulin fold-based scaffold for the generation of novel binding ligands. To obtain a suitable protein library selection system, the extracellular domain of CTLA-4 was first displayed on the surface of a filamentous phage as a fusion product of the phage coat protein p3. CTLA-4 was shown to be functionally intact by binding to its natural ligands B7-1 (CD80) and B7-2 (CD86) both in vitro and in situ. Secondly, the complementarity determining region 3 (CDR3) loop of the CTLA-4 extracellular domain was evaluated as a permissive site. We replaced the nine amino acid CDR3-like loop of CTLA-4 with the sequence XXX-RGD-XXX (where X represents any amino acid). Using phage display we selected several CTLA-4-based variants capable of binding to human αvβ3 integrin, one of which showed binding to integrins in situ. To explore the construction of bispecific molecules we also evaluated one other potential permissive site diametrically opposite the natural CDR-like loops, which was found to be tolerant of peptide insertion. Our data suggest that CTLA-4 is a suitable human scaffold for engineering single-domain molecules with one or possibly more binding specificities.
- Published
- 2000
41. Functional phage display of leech-derived tryptase inhibitor (LDTI): construction of a library and selection of thrombin inhibitors
- Author
-
Hans Fritz, Ennes A. Auerswald, Aparecida S. Tanaka, Melissa Andreia de Moraes Silva, Claudio A. M. Sampaio, Ricardo J.S. Torquato, and Maria Aparecida Eiko Noguti
- Subjects
Phage display ,Phagemid ,Mutant ,Molecular Sequence Data ,Biophysics ,Saccharomyces cerevisiae ,Biology ,Biochemistry ,law.invention ,Thrombin ,Chymases ,Structural Biology ,law ,Peptide Library ,Genetics ,medicine ,Humans ,Bacteriophages ,Amino Acid Sequence ,Cloning, Molecular ,Molecular Biology ,Base Sequence ,Dose-Response Relationship, Drug ,Models, Genetic ,Oligonucleotide ,Serine Endopeptidases ,Proteins ,Cell Biology ,Trypsin ,Molecular biology ,Kinetics ,Mutagenesis, Insertional ,Recombinant DNA ,Tryptases ,medicine.drug ,Discovery and development of direct thrombin inhibitors - Abstract
The recombinant phage antibody system pCANTAB 5E has been used to display functionally active leech-derived tryptase inhibitor (LDTI) on the tip of the filamentous M13 phage. A limited combinatorial library of 5.2×104 mutants was created with a synthetic LDTI gene, using a degenerated oligonucleotide and the pCANTAB 5E phagemid. The mutations were restricted to the P1–P4′ positions of the reactive site. Fusion phages and appropriate host strains containing the phagemids were selected after binding to thrombin and DNA sequencing. The variants LDTI-2T (K8R, I9V, S10, K11W, P12A), LDTI-5T (K8R, I9V, S10, K11S, P12L) and LDTI-10T (K8R, I9L, S10, K11D, P12I) were produced with a Saccharomyces cerevisiae expression system. The new inhibitors, LDTI-2T and -5T, prolong the blood clotting time, inhibit thrombin (Ki 302 nM and 28 nM) and trypsin (Ki 6.4 nM and 2.1 nM) but not factor Xa, plasma kallikrein or neutrophil elastase. The variant LDTI-10T binds to thrombin but does not inhibit it. The relevant reactive site sequences of the thrombin inhibiting variants showed a strong preference for arginine in position P1 (K8R) and for valine in P1′ (I9V). The data indicate further that LDTI-5T might be a model candidate for generation of active-site directed thrombin inhibitors and that LDTI in general may be useful to generate specific inhibitors suitable for a better understanding of enzyme-inhibitor interactions.
- Published
- 1999
42. Single-chain variable fragments selected on the 57-76 p21Ras neutralising epitope from phage antibody libraries recognise the parental protein
- Author
-
Hennie R. Hoogenboom, Andrew Bradbury, Susanna M. Rybak, Lidija Persic, Antonino Cattaneo, Ivo R. Horn, Persic, L, Horn, Ir, Rybak, S, Cattaneo, Antonino, Hoogenboom, Hr, and Bradbury, A.
- Subjects
Phage display ,medicine.drug_class ,Blotting, Western ,Molecular Sequence Data ,Biophysics ,Peptide ,Ras neutralizing epitope ,Enzyme-Linked Immunosorbent Assay ,Cross Reactions ,Monoclonal antibody ,Biochemistry ,Epitope ,Proto-Oncogene Proteins p21(ras) ,Epitopes ,Single-chain variable fragment ,Structural Biology ,Neutralization Tests ,Genetics ,medicine ,Phage antibody ,Amino Acid Sequence ,Bovine serum albumin ,Molecular Biology ,chemistry.chemical_classification ,biology ,Cell Biology ,Bacteriophage lambda ,Blot ,p21Ras ,chemistry ,biology.protein - Abstract
Phage antibodies have been widely prospected as an alternative to the use of monoclonal antibodies prepared by traditional means. Many monoclonal antibodies prepared against peptides are able to recognise the native proteins from which they were derived. Here we show that the same is also true for phage antibodies. We have selected a number of single-chain variable fragments (scFv) from a large phage scFv library against a peptide from the switch region II of p21Ras. This peptide is known to reside in a mobile area of the native protein and is the epitope of a well characterised monoclonal antibody. Selected scFvs were able to recognise native p21Ras in both ELISA and Western blots, indicating that peptides are also likely to be very useful in selecting from phage antibody libraries.
- Published
- 1999
43. Antibodies for all: The case for genome-wide affinity reagents
- Author
-
Sidhu, Sachdev S.
- Subjects
- *
IMMUNOGLOBULINS , *GENOMES , *HYBRIDOMAS , *BIOLOGICAL reagents , *RECOMBINANT antibodies , *THERAPEUTICS - Abstract
Abstract: For more than 30years, the production of research antibodies has been dominated by hybridoma technologies, while modern recombinant technologies have lagged behind. Here I discuss why this situation must change if we are to generate reliable, comprehensive reagent sets on a genome-wide scale, and I describe how a cultural shift in the research community could revolutionize and modernize the affinity reagent field. In turn, such a revolution would pay huge dividends by closing the gap between basic research and therapeutic development, thus enabling the development of myriad new therapies for unmet medical needs. [Copyright &y& Elsevier]
- Published
- 2012
- Full Text
- View/download PDF
44. Use of the phage display technique for detection of epitopes recognized by polyclonal rabbit gliadin antibodies
- Author
-
Awad A. Osman, Barbara Thamm, Thomas Mothes, Holm H. Uhlig, and Jens Schneider-Mergener
- Subjects
Phage display ,Immunoblotting ,Biophysics ,Enzyme-Linked Immunosorbent Assay ,Biochemistry ,Pentapeptide repeat ,Antibodies ,Gliadin ,Epitope ,Epitopes ,Antigen ,Structural Biology ,Consensus Sequence ,Genetics ,Animals ,Humans ,Bacteriophages ,Amino Acid Sequence ,Peptide library ,Molecular Biology ,Polyclonal antibody ,biology ,food and beverages ,Haplorhini ,Cell Biology ,Molecular biology ,Peptide Fragments ,Molecular Weight ,Synthetic peptide ,Polyclonal antibodies ,biology.protein ,Rabbits ,Antibody - Abstract
A random phage heptapeptide library was screened with rabbit antibodies against wheat flour proteins comprising gliadins and a small amount of low molecular weight glutenins (gli/glu). Gli/glu antibodies isolated from the sera selected different consensus sequences (CS). All CS contained tri- to pentapeptide stretches homologous to gli/glu sequences (proposed epitopes). In alpha- and gamma-type gliadins, these sequences are clustered in the N-terminal region recently suspected to be toxic for humans with celiac disease. Peptides with CS were synthesized and checked for reactivity. Only immune and no control rabbit sera reacted with synthetic peptides. One of eight human sera containing gliadin antibodies was reactive as well (4/8 peptides) but control sera were negative. Thus the phage display technique is useful for epitope screening of polyclonal antibodies even in the case of a group of homologous but diverse antigens.
- Published
- 1998
45. In vitro virus: bonding of mRNA bearing puromycin at the 3'-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro
- Author
-
Yuzuru Husimi, Etsuko Miyamoto-Sato, Naoto Nemoto, and Hiroshi Yanagawa
- Subjects
Phage display ,Reticulocytes ,Genotype ,Population ,Biophysics ,tau Proteins ,Biochemistry ,Ribosome ,Polymerase Chain Reaction ,Virus ,Evolutionary molecular engineering ,chemistry.chemical_compound ,Structural Biology ,Bonding of mRNA to protein ,Genetics ,Protein biosynthesis ,mRNA display ,Animals ,Humans ,Bacteriophages ,RNA, Messenger ,education ,Molecular Biology ,DNA Primers ,Messenger RNA ,education.field_of_study ,Cell-Free System ,Models, Genetic ,Chemistry ,Genotype assignment to phenotype ,Virion ,Genetic Variation ,In vitro virus ,Cell Biology ,Biological Evolution ,Puromycin ,Protein Biosynthesis ,Viruses ,Rabbits ,Dimerization ,Ribosomes - Abstract
Adequate means for genotype assignment to phenotype is essential in evolutionary molecular engineering. In this study, construction of 'in vitro virus' was carried out in which a genotype molecule (mRNA) covalently binds to the phenotype molecule (protein) through puromycin on the ribosome in a cell-free translation system. Bonding efficiency was approximately 10%, thus indicating a population of the in vitro virus to have approximately 10(12) protein variants, this number being 10(4) that in the phage display. The in vitro virus is useful for examining protein evolution in a test tube and the results may possibly serve as basis for a general method for selecting proteins possessing the most desirable functions.
- Published
- 1997
46. Antibodies to steroids from a small human naive IgM library
- Author
-
Stefanie Renner, Sergey Kipriyanov, Martin Welschof, Petra Rohrbach, Timo Kürschner, Michael Braunagel, Melvyn Little, and Heinz Dörsam
- Subjects
Phage display ,Sequence analysis ,Molecular Sequence Data ,Biophysics ,Immunoglobulin Variable Region ,Immunoglobulin light chain ,Biochemistry ,chemistry.chemical_compound ,Structural Biology ,Peptide Library ,Progesterone receptor ,Genetics ,Escherichia coli ,Digoxigenin ,Single chain antibody ,Anti-steroid antibody ,Humans ,Bacteriophages ,Testosterone ,Lymphocytes ,Cloning, Molecular ,Peptide library ,Molecular Biology ,Immunoglobulin Fragments ,Progesterone ,Human IgM repertoire ,Gene Library ,biology ,Estradiol ,Molecular Structure ,Cell Biology ,Sequence Analysis, DNA ,Virology ,Molecular biology ,Antibody library ,Recombinant Proteins ,Kinetics ,chemistry ,Immunoglobulin M ,biology.protein ,Steroids ,Antibody ,Single-Chain Antibodies ,Protein Binding - Abstract
Human antibodies specific for digoxigenin, estradiol, testosterone and progesterone have been isolated from a small combinatorial IgM repertoire (4×107) of single chain antibodies (scFv). The affinities of both the anti-estradiol and anti-progesterone scFv were approximately 108 M−1. Naive IgM genes appeared to be highly represented, since only the heavy chain variable domain of the anti estradiol antibody contained differences to corresponding germline sequences. The light chain variable domain of the progesterone receptor was also identical to a germline sequence, showing that it is possible for completely naive antibodies to bind steroids with affinities comparable to those obtained after a secondary immune response.
- Published
- 1997
47. Identification of novel heparin-binding domains of vitronectin
- Author
-
Olin D. Liang, Klaus T. Preissner, Gursharan S. Chhatwal, and Sylvia Rosenblatt
- Subjects
Phage display ,Molecular Sequence Data ,Biophysics ,Serum protein ,Biology ,Biochemistry ,Structural Biology ,Peptide Library ,Genetics ,medicine ,Amino Acid Sequence ,Vitronectin ,Cell adhesion ,Molecular Biology ,chemistry.chemical_classification ,Binding Sites ,Heparin ,Cell Biology ,Peptide Fragments ,Recombinant Proteins ,Amino acid ,body regions ,chemistry ,biology.protein ,medicine.drug - Abstract
Vitronectin is a multifunctional serum protein which provides a unique regulatory link between cell adhesion, humoral defense mechanism and the hemostatic system, and the heparin-binding properties of vitronectin are thought to have participated in various functional aspects. In addition to the carboxy-terminal glycosaminoglycan-binding motif, we report on two novel heparin-binding domains which were identified using phage display technique. One heparin-binding domain is located between amino acids Asp82 and Cys137 at the end of the connector region, while the other is in the second hemopexin-type repeat, between amino acids Lys175 and Asp219 of the vitronectin molecule. Our findings may shed new light to the activities of vitronectin and its binding to cells, which could not be explained solely on the basis of the known heparin-binding domain.
- Published
- 1997
48. Use of phage display for isolation and characterization of single-chain variable fragments against dihydroflavonol 4-reductase from Petunia hybrida
- Author
-
Emmanuel S. Buys, Anna Depicker, Tom Gerats, Geert De Jaeger, Myriam De Neve, Rainer Fischer, Chris De Wilde, Anne-Marie Bruyns, Marc Van Montagu, and Dominique Eeckhout
- Subjects
Phage display ,Molecular Sequence Data ,Biophysics ,Biology ,medicine.disease_cause ,Biochemistry ,DNA sequencing ,law.invention ,Immunomodulation ,Mice ,Western blot ,Single-chain variable fragment ,Structural Biology ,law ,Genetics ,medicine ,Escherichia coli ,Animals ,Bacteriophages ,Amino Acid Sequence ,Cloning, Molecular ,Panning (camera) ,Molecular Biology ,Polymerase chain reaction ,DNA Primers ,medicine.diagnostic_test ,Base Sequence ,Sequence Homology, Amino Acid ,Cell Biology ,Petunia hybrida ,Plants ,Molecular biology ,Dihydroflavonol 4-reductase ,Alcohol Oxidoreductases ,Recombinant antibody ,Recombinant DNA - Abstract
To isolate specific single-chain variable (scFv) fragments against dihydroflavonol 4-reductase (DFR) from Petunia hybrida the phage display technology was used. DFR was overproduced in Escherichia coli, purified and used for immunization. From DFR-immunized mice, a phage display library was made starting from spleen mRNA using an optimized set of primers for VH and VL amplification. Several rounds of panning against recombinant DFR yielded five different scFv fragments, confirmed by subsequent DNA sequencing. They all specifically bound to recombinant DFR in ELISA and DFR in flower extracts on Western blot. These results show that phage display is a promising technology in plant molecular biology to obtain specific recombinant antibodies not only for ELISA and Western blot but also for in vivo applications in the long run. © 1997 Federation of European Biochemical Societies.
- Published
- 1997
49. A model phage display subtraction method with potential for analysis of differential gene expression
- Author
-
Brian F.C. Clark, Svend Kjær, Nils J.V. Hansen, Liselotte Kahns, Brian Stausbøl-Grøn, Peter Kristensen, and Troels Wind
- Subjects
Phage display ,Subtraction method ,Selection strategy ,Biophysics ,Immunoglobulin Variable Region ,lac operon ,Antibody engineering ,Gene Expression ,Enzyme-Linked Immunosorbent Assay ,Biochemistry ,Antibodies ,Cell Line ,Phage display subtraction ,Structural Biology ,Antibody Specificity ,Gene expression ,Genetics ,Tumor Cells, Cultured ,Animals ,Humans ,Bacteriophages ,Antigens ,Molecular Biology ,Melanoma ,Selection (genetic algorithm) ,Single-chain Fv fragment ,Subtractive color ,biology ,Competitive selection ,Proteins ,Cell Biology ,Protein Biosynthesis ,biology.protein ,Phage antibody library ,Antibody ,Information Systems - Abstract
In order to establish a subtractive procedure that makes it possible to enrich selectively phage displayed antibodies directed against proteins constituting a difference between two populations of cells, a competitive selection strategy utilising two solid phases was developed and tested. Antibodies recognising a defined difference between two otherwise identical protein mixtures were isolated and their specificity confirmed. To test further the efficacy of selection inhibition during the competitive selections, selections towards a total cell extract were performed with and without competition from the same extract. An analysis of the resulting phage antibodies confirmed the subtractive nature of the system described.
- Published
- 1996
50. A monoclonal antibody that causes the heterotrimeric G-protein G(o) to release its beta gamma subunits
- Author
-
Hidde L. Ploegh, Jonathan Oleinick, and Mamadi Yilla
- Subjects
Monoclonal antibody ,Phage display ,medicine.drug_class ,Guanine ,Molecular Sequence Data ,Biophysics ,Biochemistry ,Epitope ,chemistry.chemical_compound ,Guanine nucleotide ,Structural Biology ,GTP-Binding Proteins ,Heterotrimeric G protein ,Trimeric G-protein ,Genetics ,medicine ,Animals ,Nucleotide ,Amino Acid Sequence ,Antibody-induced dissociation ,Molecular Biology ,chemistry.chemical_classification ,Chemistry ,Antibodies, Monoclonal ,Cell Biology ,Guanine Nucleotides ,Guanosine 5'-O-(3-Thiotriphosphate) ,G12/G13 alpha subunits ,Cattle ,Signal transduction ,Epitope Mapping - Abstract
Heterotrimeric (alpha beta gamma) guanine nucleotide binding proteins (G-proteins) dissociate into their constituent subunits in the course of signal transduction. Exposure of the G-protein G(o) to the alpha(o)-specific monoclonal antibody 3E7 results in recovery of alpha(o) alone. We identified the 3E7 epitope as ERSKAIEKNL (positions 14-23) using synthetic peptides and phage display. G(o) isolated with alpha(o)-specific monoclonal antibodies MONO and 3C2 dissociates and releases its beta gamma subunits when exposed to 3E7. Exposure to 3E7, but not MONO or 3C2, results in the displacement of beta gamma from trimers, in the absence of added activators of G-proteins (GTPgammaS, Mg2+AlF4-). We propose that stable binding of 3E7 to alpha(o) requires displacement of beta-gamma and occurs in the absence of guanine nucleotide exchange.
- Published
- 1996
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.